[English] 日本語
Yorodumi
- PDB-7k17: Re-refined crystal structure of DNA-dependent protein kinase cata... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7k17
TitleRe-refined crystal structure of DNA-dependent protein kinase catalytic subunit complexed with Ku80 C-terminal helix
Components
  • DNA-dependent protein kinase catalytic subunit
  • X-ray repair cross-complementing protein 5
KeywordsDNA BINDING PROTEIN / NHEJ / V(D)J recombination / DNA repair
Function / homology
Function and homology information


Ku70:Ku80 complex / negative regulation of t-circle formation / DNA end binding / small-subunit processome assembly / DNA-dependent protein kinase-DNA ligase 4 complex / nonhomologous end joining complex / regulation of smooth muscle cell proliferation / Cytosolic sensors of pathogen-associated DNA / nuclear telomere cap complex / IRF3-mediated induction of type I IFN ...Ku70:Ku80 complex / negative regulation of t-circle formation / DNA end binding / small-subunit processome assembly / DNA-dependent protein kinase-DNA ligase 4 complex / nonhomologous end joining complex / regulation of smooth muscle cell proliferation / Cytosolic sensors of pathogen-associated DNA / nuclear telomere cap complex / IRF3-mediated induction of type I IFN / U3 snoRNA binding / regulation of telomere maintenance / recombinational repair / protein localization to chromosome, telomeric region / 2-LTR circle formation / telomeric repeat DNA binding / DNA 3'-5' helicase / 3'-5' DNA helicase activity / ATP-dependent activity, acting on DNA / telomere maintenance via telomerase / activation of innate immune response / telomere maintenance / DNA helicase activity / DNA-(apurinic or apyrimidinic site) lyase / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / site of DNA damage / cellular response to gamma radiation / small-subunit processome / Nonhomologous End-Joining (NHEJ) / protein-DNA complex / double-strand break repair via nonhomologous end joining / enzyme activator activity / double-strand break repair / double-stranded DNA binding / DNA recombination / secretory granule lumen / damaged DNA binding / chromosome, telomeric region / transcription cis-regulatory region binding / ribonucleoprotein complex / innate immune response / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / DNA damage response / Neutrophil degranulation / nucleolus / protein-containing complex binding / ATP hydrolysis activity / protein-containing complex / DNA binding / DNA-templated transcription / RNA binding / extracellular region / nucleoplasm / ATP binding / membrane / nucleus / cytosol
Similarity search - Function
Ku, C-terminal / Ku, C-terminal domain superfamily / Ku C terminal domain like / Ku80 / Ku70/Ku80 C-terminal arm / Ku70/Ku80 C-terminal arm / Ku70/Ku80, N-terminal alpha/beta / Ku70/Ku80 N-terminal alpha/beta domain / Ku70/Ku80 beta-barrel domain / Ku70 and Ku80 are 70kDa and 80kDa subunits of the Lupus Ku autoantigen ...Ku, C-terminal / Ku, C-terminal domain superfamily / Ku C terminal domain like / Ku80 / Ku70/Ku80 C-terminal arm / Ku70/Ku80 C-terminal arm / Ku70/Ku80, N-terminal alpha/beta / Ku70/Ku80 N-terminal alpha/beta domain / Ku70/Ku80 beta-barrel domain / Ku70 and Ku80 are 70kDa and 80kDa subunits of the Lupus Ku autoantigen / Ku70/Ku80 beta-barrel domain / SPOC-like, C-terminal domain superfamily / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily
Similarity search - Domain/homology
DNA repair protein Ku80
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.3 Å
AuthorsChen, X. / Gellert, M. / Yang, W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) United States
CitationJournal: Science / Year: 2017
Title: DNA-PKcs structure suggests an allosteric mechanism modulating DNA double-strand break repair.
Authors: Sibanda, B.L. / Chirgadze, D.Y. / Ascher, D.B. / Blundell, T.L.
History
DepositionSep 7, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 6, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 3, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Remark 0THIS ENTRY 7K17 REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN 5LUQ, DETERMINED BY B.L. ...THIS ENTRY 7K17 REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN 5LUQ, DETERMINED BY B.L.Sibanda, D.Y.Chirgadze, D.B.Ascher, T.L.Blundell

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA-dependent protein kinase catalytic subunit
B: DNA-dependent protein kinase catalytic subunit
D: X-ray repair cross-complementing protein 5
C: X-ray repair cross-complementing protein 5


Theoretical massNumber of molelcules
Total (without water)947,9414
Polymers947,9414
Non-polymers00
Water00
1
A: DNA-dependent protein kinase catalytic subunit
C: X-ray repair cross-complementing protein 5


Theoretical massNumber of molelcules
Total (without water)473,9712
Polymers473,9712
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-11 kcal/mol
Surface area166350 Å2
MethodPISA
2
B: DNA-dependent protein kinase catalytic subunit
D: X-ray repair cross-complementing protein 5


Theoretical massNumber of molelcules
Total (without water)473,9712
Polymers473,9712
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-10 kcal/mol
Surface area162840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.120, 132.640, 296.590
Angle α, β, γ (deg.)90.000, 105.530, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111VALVALTHRTHR(chain 'A' and (resid 8 through 61 or (resid 62...AA8 - 2358 - 235
121ASPASPTHRTHR(chain 'A' and (resid 8 through 61 or (resid 62...AA241 - 400241 - 400
131VALVALVALVAL(chain 'A' and (resid 8 through 61 or (resid 62...AA407 - 496407 - 496
141VALVALLEULEU(chain 'A' and (resid 8 through 61 or (resid 62...AA521 - 545521 - 545
151ASNASNTHRTHR(chain 'A' and (resid 8 through 61 or (resid 62...AA561 - 587561 - 587
161METMETGLUGLU(chain 'A' and (resid 8 through 61 or (resid 62...AA602 - 684602 - 684
171TYRTYRLYSLYS(chain 'A' and (resid 8 through 61 or (resid 62...AA701 - 801701 - 801
181ILEILEGLNGLN(chain 'A' and (resid 8 through 61 or (resid 62...AA846 - 947846 - 947
191PROPROCYSCYS(chain 'A' and (resid 8 through 61 or (resid 62...AA956 - 1229956 - 1229
1101GLNGLNALAALA(chain 'A' and (resid 8 through 61 or (resid 62...AA1251 - 13021251 - 1302
1111SERSERTHRTHR(chain 'A' and (resid 8 through 61 or (resid 62...AA1323 - 13511323 - 1351
1121LEULEUPROPRO(chain 'A' and (resid 8 through 61 or (resid 62...AA1359 - 14931359 - 1493
1131PROPROVALVAL(chain 'A' and (resid 8 through 61 or (resid 62...AA1501 - 15371501 - 1537
1141GLYGLYSERSER(chain 'A' and (resid 8 through 61 or (resid 62...AA1556 - 16571556 - 1657
1151HISHISVALVAL(chain 'A' and (resid 8 through 61 or (resid 62...AA1665 - 19941665 - 1994
1161SERSERTHRTHR(chain 'A' and (resid 8 through 61 or (resid 62...AA2034 - 20472034 - 2047
1171GLUGLULEULEU(chain 'A' and (resid 8 through 61 or (resid 62...AA2082 - 21082082 - 2108
1181PROPROSERSER(chain 'A' and (resid 8 through 61 or (resid 62...AA2119 - 25932119 - 2593
1191UNKUNKUNKUNK(chain 'A' and (resid 8 through 61 or (resid 62...AA2606 - 26132601 - 2608
1201UNKUNKUNKUNK(chain 'A' and (resid 8 through 61 or (resid 62...AA2739 - 27402610 - 2611
1211UNKUNKUNKUNK(chain 'A' and (resid 8 through 61 or (resid 62...AA2742 - 27642613 - 2635
1221ASPASPASPASP(chain 'A' and (resid 8 through 61 or (resid 62...AA27792637
1231GLNGLNLEULEU(chain 'A' and (resid 8 through 61 or (resid 62...AA2784 - 28972642 - 2755
1241ASPASPTHRTHR(chain 'A' and (resid 8 through 61 or (resid 62...AA2919 - 31982777 - 3056
1251ASPASPLEULEU(chain 'A' and (resid 8 through 61 or (resid 62...AA3226 - 33623084 - 3220
1261ASPASPGLNGLN(chain 'A' and (resid 8 through 61 or (resid 62...AA3369 - 33903227 - 3248
1271ALAALAGLUGLU(chain 'A' and (resid 8 through 61 or (resid 62...AA3406 - 34293264 - 3287
1281GLNGLNMETMET(chain 'A' and (resid 8 through 61 or (resid 62...AA3440 - 41283298 - 3986
211VALVALTHRTHR(chain 'B' and (resid 8 through 53 or (resid 54...BB8 - 2358 - 235
221ASPASPTHRTHR(chain 'B' and (resid 8 through 53 or (resid 54...BB241 - 400241 - 400
231VALVALVALVAL(chain 'B' and (resid 8 through 53 or (resid 54...BB407 - 496407 - 496
241VALVALLEULEU(chain 'B' and (resid 8 through 53 or (resid 54...BB521 - 545521 - 545
251ASNASNTHRTHR(chain 'B' and (resid 8 through 53 or (resid 54...BB561 - 587561 - 587
261METMETGLUGLU(chain 'B' and (resid 8 through 53 or (resid 54...BB602 - 684602 - 684
271TYRTYRLYSLYS(chain 'B' and (resid 8 through 53 or (resid 54...BB701 - 801701 - 801
281ILEILEGLNGLN(chain 'B' and (resid 8 through 53 or (resid 54...BB846 - 947846 - 947
291PROPROCYSCYS(chain 'B' and (resid 8 through 53 or (resid 54...BB956 - 1229956 - 1229
2101GLNGLNALAALA(chain 'B' and (resid 8 through 53 or (resid 54...BB1251 - 13021251 - 1302
2111SERSERTHRTHR(chain 'B' and (resid 8 through 53 or (resid 54...BB1323 - 13511323 - 1351
2121LEULEUPROPRO(chain 'B' and (resid 8 through 53 or (resid 54...BB1359 - 14931359 - 1493
2131PROPROVALVAL(chain 'B' and (resid 8 through 53 or (resid 54...BB1501 - 15371501 - 1537
2141GLYGLYSERSER(chain 'B' and (resid 8 through 53 or (resid 54...BB1556 - 16571556 - 1657
2151HISHISVALVAL(chain 'B' and (resid 8 through 53 or (resid 54...BB1665 - 19941665 - 1994
2161SERSERTHRTHR(chain 'B' and (resid 8 through 53 or (resid 54...BB2034 - 20472034 - 2047
2171GLUGLULEULEU(chain 'B' and (resid 8 through 53 or (resid 54...BB2082 - 21082082 - 2108
2181PROPROSERSER(chain 'B' and (resid 8 through 53 or (resid 54...BB2119 - 25932119 - 2593
2191UNKUNKUNKUNK(chain 'B' and (resid 8 through 53 or (resid 54...BB2603 - 26102599 - 2606
2201UNKUNKUNKUNK(chain 'B' and (resid 8 through 53 or (resid 54...BB2612 - 26132608 - 2609
2211UNKUNKUNKUNK(chain 'B' and (resid 8 through 53 or (resid 54...BB2740 - 27622611 - 2633
2221UNKUNKUNKUNK(chain 'B' and (resid 8 through 53 or (resid 54...BB27642635
2231GLNGLNLEULEU(chain 'B' and (resid 8 through 53 or (resid 54...BB2784 - 28972642 - 2755
2241ASPASPTHRTHR(chain 'B' and (resid 8 through 53 or (resid 54...BB2919 - 31982777 - 3056
2251ASPASPLEULEU(chain 'B' and (resid 8 through 53 or (resid 54...BB3226 - 33623084 - 3220
2261ASPASPGLNGLN(chain 'B' and (resid 8 through 53 or (resid 54...BB3369 - 33903227 - 3248
2271ALAALAGLUGLU(chain 'B' and (resid 8 through 53 or (resid 54...BB3406 - 34293264 - 3287
2281GLNGLNMETMET(chain 'B' and (resid 8 through 53 or (resid 54...BB3440 - 41283298 - 3986
112ASPASPILEILEchain 'C'CD724 - 732184 - 192
212ASPASPILEILEchain 'D'DC724 - 732184 - 192

NCS ensembles :
ID
1
2

-
Components

#1: Protein DNA-dependent protein kinase catalytic subunit / DNA-PKcs / DNPK1 / p460


Mass: 452515.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: non-specific serine/threonine protein kinase
#2: Protein X-ray repair cross-complementing protein 5 / 86 kDa subunit of Ku antigen / ATP-dependent DNA helicase 2 subunit 2 / ATP-dependent DNA helicase ...86 kDa subunit of Ku antigen / ATP-dependent DNA helicase 2 subunit 2 / ATP-dependent DNA helicase II 80 kDa subunit / CTC box-binding factor 85 kDa subunit / CTCBF / DNA repair protein XRCC5 / Ku80 / Ku86 / Lupus Ku autoantigen protein p86 / Nuclear factor IV / Thyroid-lupus autoantigen / TLAA / X-ray repair complementing defective repair in Chinese hamster cells 5 (double-strand-break rejoining)


Mass: 21454.877 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XRCC5, G22P2 / Production host: Escherichia coli (E. coli)
References: UniProt: P13010, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Sequence detailsThe complete sample sequence of DNA-dependent protein kinase catalytic subunit is ...The complete sample sequence of DNA-dependent protein kinase catalytic subunit is MAGSGAGVRCSLLRLQETLSAADRCGAALAGHQLIRGLGQECVLSSSPAVLALQTSLVFS RDFGLLVFVRKSLNSIEFRECREEILKFLCIFLEKMGQKIAPYSVEIKNTCTSVYTKDRA AKCKIPALDLLIKLLQTFRSSRLMDEFKIGELFSKFYGELALKKKIPDTVLEKVYELLGL LGEVHPSEMINNAENLFRAFLGELKTQMTSAVREPKLPVLAGCLKGLSSLLCNFTKSMEE DPQTSREIFNFVLKAIRPQIDLKRYAVPSAGLRLFALHASQFSTCLLDNYVSLFEVLLKW CAHTNVELKKAALSALESFLKQVSNMVAKNAEMHKNKLQYFMEQFYGIIRNVDSNNKELS IAIRGYGLFAGPCKVINAKDVDFMYVELIQRCKQMFLTQTDTGDDRVYQMPSFLQSVASV LLYLDTVPEVYTPVLEHLVVMQIDSFPQYSPKMQLVCCRAIVKVFLALAAKGPVLRNCIS TVVHQGLIRICSKPVVLPKGPESESEDHRASGEVRTGKWKVPTYKDYVDLFRHLLSSDQM MDSILADEAFFSVNSSSESLNHLLYDEFVKSVLKIVEKLDLTLEIQTVGEQENGDEAPGV WMIPTSDPAANLHPAKPKDFSAFINLVEFCREILPEKQAEFFEPWVYSFSYELILQSTRL PLISGFYKLLSITVRNAKKIKYFEGVSPKSLKHSPEDPEKYSCFALFVKFGKEVAVKMKQ YKDELLASCLTFLLSLPHNIIELDVRAYVPALQMAFKLGLSYTPLAEVGLNALEEWSIYI DRHVMQPYYKDILPCLDGYLKTSALSDETKNNWEVSALSRAAQKGFNKVVLKHLKKTKNL SSNEAISLEEIRIRVVQMLGSLGGQINKNLLTVTSSDEMMKSYVAWDREKRLSFAVPFRE MKPVIFLDVFLPRVTELALTASDRQTKVAACELLHSMVMFMLGKATQMPEGGQGAPPMYQ LYKRTFPVLLRLACDVDQVTRQLYEPLVMQLIHWFTNNKKFESQDTVALLEAILDGIVDP VDSTLRDFCGRCIREFLKWSIKQITPQQQEKSPVNTKSLFKRLYSLALHPNAFKRLGASL AFNNIYREFREEESLVEQFVFEALVIYMESLALAHADEKSLGTIQQCCDAIDHLCRIIEK KHVSLNKAKKRRLPRGFPPSASLCLLDLVKWLLAHCGRPQTECRHKSIELFYKFVPLLPG NRSPNLWLKDVLKEEGVSFLINTFEGGGCGQPSGILAQPTLLYLRGPFSLQATLCWLDLL LAALECYNTFIGERTVGALQVLGTEAQSSLLKAVAFFLESIAMHDIIAAEKCFGTGAAGN RTSPQEGERYNYSKCTVVVRIMEFTTTLLNTSPEGWKLLKKDLCNTHLMRVLVQTLCEPA SIGFNIGDVQVMAHLPDVCVNLMKALKMSPYKDILETHLREKITAQSIEELCAVNLYGPD AQVDRSRLAAVVSACKQLHRAGLLHNILPSQSTDLHHSVGTELLSLVYKGIAPGDERQCL PSLDLSCKQLASGLLELAFAFGGLCERLVSLLLNPAVLSTASLGSSQGSVIHFSHGEYFY SLFSETINTELLKNLDLAVLELMQSSVDNTKMVSAVLNGMLDQSFRERANQKHQGLKLAT TILQHWKKCDSWWAKDSPLETKMAVLALLAKILQIDSSVSFNTSHGSFPEVFTTYISLLA DTKLDLHLKGQAVTLLPFFTSLTGGSLEELRRVLEQLIVAHFPMQSREFPPGTPRFNNYV DCMKKFLDALELSQSPMLLELMTEVLCREQQHVMEELFQSSFRRIARRGSCVTQVGLLES VYEMFRKDDPRLSFTRQSFVDRSLLTLLWHCSLDALREFFSTIVVDAIDVLKSRFTKLNE STFDTQITKKMGYYKILDVMYSRLPKDDVHAKESKINQVFHGSCITEGNELTKTLIKLCY DAFTENMAGENQLLERRRLYHCAAYNCAISVICCVFNELKFYQGFLFSEKPEKNLLIFEN LIDLKRRYNFPVEVEVPMERKKKYIEIRKEAREAANGDSDGPSYMSSLSYLADSTLSEEM SQFDFSTGVQSYSYSSQDPRPATGRFRRREQRDPTVHDDVLELEMDELNRHECMAPLTAL VKHMHRSLGPPQGEEDSVPRDLPSWMKFLHGKLGNPIVPLNIRLFLAKLVINTEEVFRPY AKHWLSPLLQLAASENNGGEGIHYMVVEIVATILSWTGLATPTGVPKDEVLANRLLNFLM KHVFHPKRAVFRHNLEIIKTLVECWKDCLSIPYRLIFEKFSGKDPNSKDNSVGIQLLGIV MANDLPPYDPQCGIQSSEYFQALVNNMSFVRYKEVYAAAAEVLGLILRYVMERKNILEES LCELVAKQLKQHQNTMEDKFIVCLNKVTKSFPPLADRFMNAVFFLLPKFHGVLKTLCLEV VLCRVEGMTELYFQLKSKDFVQVMRHRDDERQKVCLDIIYKMMPKLKPVELRELLNPVVE FVSHPSTTCREQMYNILMWIHDNYRDPESETDNDSQEIFKLAKDVLIQGLIDENPGLQLI IRNFWSHETRLPSNTLDRLLALNSLYSPKIEVHFLSLATNFLLEMTSMSPDYPNPMFEHP LSECEFQEYTIDSDWRFRSTVLTPMFVETQASQGTLQTRTQEGSLSARWPVAGQIRATQQ QHDFTLTQTADGRSSFDWLTGSSTDPLVDHTSPSSDSLLFAHKRSERLQRAPLKSVGPDF GKKRLGLPGDEVDNKVKGAAGRTDLLRLRRRFMRDQEKLSLMYARKGVAEQKREKEIKSE LKMKQDAQVVLYRSYRHGDLPDIQIKHSSLITPLQAVAQRDPIIAKQLFSSLFSGILKEM DKFKTLSEKNNITQKLLQDFNRFLNTTFSFFPPFVSCIQDISCQHAALLSLDPAAVSAGC LASLQQPVGIRLLEEALLRLLPAELPAKRVRGKARLPPDVLRWVELAKLYRSIGEYDVLR GIFTSEIGTKQITQSALLAEARSDYSEAAKQYDEALNKQDWVDGEPTEAEKDFWELASLD CYNHLAEWKSLEYCSTASIDSENPPDLNKIWSEPFYQETYLPYMIRSKLKLLLQGEADQS LLTFIDKAMHGELQKAILELHYSQELSLLYLLQDDVDRAKYYIQNGIQSFMQNYSSIDVL LHQSRLTKLQSVQALTEIQEFISFISKQGNLSSQVPLKRLLNTWTNRYPDAKMDPMNIWD DIITNRCFFLSKIEEKLTPLPEDNSMNVDQDGDPSDRMEVQEQEEDISSLIRSCKFSMKM KMIDSARKQNNFSLAMKLLKELHKESKTRDDWLVSWVQSYCRLSHCRSRSQGCSEQVLTV LKTVSLLDENNVSSYLSKNILAFRDQNILLGTTYRIIANALSSEPACLAEIEEDKARRIL ELSGSSSEDSEKVIAGLYQRAFQHLSEAVQAAEEEAQPPSWSCGPAAGVIDAYMTLADFC DQQLRKEEENASVIDSAELQAYPALVVEKMLKALKLNSNEARLKFPRLLQIIERYPEETL SLMTKEISSVPCWQFISWISHMVALLDKDQAVAVQHSVEEITDNYPQAIVYPFIISSESY SFKDTSTGHKNKEFVARIKSKLDQGGVIQDFINALDQLSNPELLFKDWSNDVRAELAKTP VNKKNIEKMYERMYAALGDPKAPGLGAFRRKFIQTFGKEFDKHFGKGGSKLLRMKLSDFN DITNMLLLKMNKDSKPPGNLKECSPWMSDFKVEFLRNELEIPGQYDGRGKPLPEYHVRIA GFDERVTVMASLRRPKRIIIRGHDEREHPFLVKGGEDLRQDQRVEQLFQVMNGILAQDSA CSQRALQLRTYSVVPMTSRLGLIEWLENTVTLKDLLLNTMSQEEKAAYLSDPRAPPCEYK DWLTKMSGKHDVGAYMLMYKGANRTETVTSFRKRESKVPADLLKRAFVRMSTSPEAFLAL RSHFASSHALICISHWILGIGDRHLNNFMVAMETGGVIGIDFGHAFGSATQFLPVPELMP FRLTRQFINLMLPMKETGLMYSIMVHALRAFRSDPGLLTNTMDVFVKEPSFDWKNFEQKM LKKGGSWIQEINVAEKNWYPRQKICYAKRKLAGANPAVITCDELLLGHEKAPAFRDYVAV ARGSKDHNIRAQEPESGLSEETQVKCLMDQATDPNILGRTWEGWEPWM

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Description
13.8668.15Author used the sf data from entry 5LUQ
23.8668.15Author used the sf data from entry 5LUQ
Crystal grow
Temperature (K)Crystal-IDMethodDetails
2931vapor diffusion, hanging drop0.1 M Bis-Tris, 200 mM NaCl, 30% glycerol, 10 mM EDTA, 18% PEG 8000
2932vapor diffusion, hanging drop0.1 M Bis-Tris, 200 mM NaCl, 30% glycerol, 10 mM EDTA, 8% PEG 8000

-
Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21002N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID2910.9791
SYNCHROTRONESRF ID23-120.9791
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M-F1PIXELMay 23, 2012
DECTRIS PILATUS 6M-F2PIXELJun 25, 2011
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
21
ReflectionResolution: 4.3→49.918 Å / Num. obs: 86508 / % possible obs: 97.8 % / Redundancy: 35.2 % / Biso Wilson estimate: 185.23 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 15.4
Reflection shellResolution: 4.3→4.4075 Å / Rmerge(I) obs: 0.936 / Num. unique obs: 0

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PHENIX1.14_3260phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7K0Y

7k0y


Resolution: 4.3→49.92 Å / SU ML: 0.7829 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 41.5014 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3353 1978 2.34 %
Rwork0.2859 82547 -
obs0.287 84525 97.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 217.04 Å2
Refinement stepCycle: LAST / Resolution: 4.3→49.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms56895 0 0 0 56895
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00458016
X-RAY DIFFRACTIONf_angle_d0.861178589
X-RAY DIFFRACTIONf_chiral_restr0.04619116
X-RAY DIFFRACTIONf_plane_restr0.00549972
X-RAY DIFFRACTIONf_dihedral_angle_d21.596721262
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.3-4.410.44281340.40485459X-RAY DIFFRACTION91.03
4.41-4.530.39251350.38385634X-RAY DIFFRACTION94.88
4.53-4.660.41961400.36355746X-RAY DIFFRACTION95.75
4.66-4.810.3931400.36755784X-RAY DIFFRACTION96.61
4.81-4.980.39371420.3655844X-RAY DIFFRACTION97.16
4.98-5.180.43291350.36055858X-RAY DIFFRACTION97.91
5.18-5.420.37051450.36755942X-RAY DIFFRACTION98.61
5.42-5.70.39361400.36925940X-RAY DIFFRACTION98.96
5.7-6.060.37251340.37546011X-RAY DIFFRACTION99.29
6.06-6.530.39621470.36725984X-RAY DIFFRACTION99.51
6.53-7.180.42381420.33356007X-RAY DIFFRACTION99.87
7.18-8.220.33221440.27236060X-RAY DIFFRACTION100
8.22-10.340.27071480.18776087X-RAY DIFFRACTION99.98
10.34-49.920.25331520.20956191X-RAY DIFFRACTION99.56
Refinement TLS params.Method: refined / Origin x: 21.7139499133 Å / Origin y: 21.6150386642 Å / Origin z: 73.977301847 Å
111213212223313233
T1.96910464944 Å20.23548057605 Å20.150643938936 Å2-1.29490198843 Å20.0785417600262 Å2--2.12038490571 Å2
L0.146615826474 °2-0.0775742632931 °2-0.0602368063791 °2-0.0467593383949 °20.0605389396786 °2--0.0563880726578 °2
S-0.118135563901 Å °-0.0474345978314 Å °0.00877954087073 Å °0.131806639157 Å °0.037162536322 Å °0.00270294463178 Å °-0.0434187020948 Å °0.0630773563929 Å °0.099795708351 Å °
Refinement TLS groupSelection details: all

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more